User Tools

Site Tools


exercises:2018_ethz_mmm:lennard_jones_cluster_2018

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision Both sides next revision
exercises:2018_ethz_mmm:lennard_jones_cluster_2018 [2018/02/23 08:34]
dpasserone
exercises:2018_ethz_mmm:lennard_jones_cluster_2018 [2018/02/23 08:37]
dpasserone
Line 153: Line 153:
   - <​code>​ python stein.py file.xyz </​code>​You will be asked the cutoff radius for the neighbors, it is **1.391** in sigma units. **You should input it in Angstrom**. You will also be asked **"​value of l"** This means the symmetry of the order parameter, which is **l=4** in this case.   - <​code>​ python stein.py file.xyz </​code>​You will be asked the cutoff radius for the neighbors, it is **1.391** in sigma units. **You should input it in Angstrom**. You will also be asked **"​value of l"** This means the symmetry of the order parameter, which is **l=4** in this case.
   - before running the simulation, copy the input coordinate file into in.xyz <​code>​cp fcc_rand.xyz in.xyz</​code>​   - before running the simulation, copy the input coordinate file into in.xyz <​code>​cp fcc_rand.xyz in.xyz</​code>​
 +  - Before running cp2k, check if the file **OPT-pos-1.xyz** is already present from a previous run. In that case remove or delete it accordingly. It contains the trajectory of the optimization.
   - run cp2k  <​code>​cp2k.ssmp -i geo_opt.inp | tee geo_opt.out </​code>​ (to see the output on the screen as well), or **AS AN ALTERNATIVE** <​code>​cp2k.ssmp -i geo_opt.inp > geo_opt.out </​code>​ (to retain the output in the geo_opt.out file only)    - run cp2k  <​code>​cp2k.ssmp -i geo_opt.inp | tee geo_opt.out </​code>​ (to see the output on the screen as well), or **AS AN ALTERNATIVE** <​code>​cp2k.ssmp -i geo_opt.inp > geo_opt.out </​code>​ (to retain the output in the geo_opt.out file only) 
   - in the output file, grep the final energy <​code>​grep "​ENERGY|“ geo_opt.out</​code>​ and transform it in the unit of the paper (epsilon units)   - in the output file, grep the final energy <​code>​grep "​ENERGY|“ geo_opt.out</​code>​ and transform it in the unit of the paper (epsilon units)
exercises/2018_ethz_mmm/lennard_jones_cluster_2018.txt · Last modified: 2018/04/14 14:50 by oschuett